I designed a custom board with an ATMEGA2560 MCU. In order to facilitate "electronics debugging" I'm soldering components as I need.

At this moment, as key components, I have the MCU, the 16MHz crystal, ICSP header and FTDI FT232RL. I managed to burn the bootloader (with an AVRISP MKII connected to the ICSP header) with settings as shown in uploaded images. I can also burn sketches code as .hex files using the AVRISP MKII as well.

The problem occurs when trying to upload sketches directly from Arduino 0022 IDE to the FT232RL on the board. The weird part here is that I can only upload the program immediately after burning bootloader with AVRISP. Any other tries result on a avrdude timeout.